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Originally Posted by
OhioLefty 
After I run Audyssey, it set the mains, center and surrounds to "Full Band" and sets the subs at -9db.
It's important to understand that Audyssey isn't setting any of your speakers to small vs large. Audyssey just measures and then the receiver manufacturer decides to call the speaker "full band". If you followed the Audyssey setup guide (or read
the Audyssey FAQ) you will see that Audyssey specifically recommends taking them off full band and setting them to "small" (on the Onkyo that means assigning a crossover).
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If your AVR manufacturer sets your speakers to Large then all content below the crossover frequency is lost as it is not redirected to the subwoofer. Audyssey recommends changing the speaker setting to Small manually after the calibration is finished.
Changing your speakers to small allows bass to be effectively routed to your shiny new 12" subwoofer. It also allows the other speakers to play louder and cleaner (because they aren't reproducing bass that they can't handle) and lets your amp perform better because the subwoofer's amp is handling the most difficult loads.
Additionally, the MultEQ XT in your 705 has much higher resolution filters on the subwoofer channel, so letting your sub handle the bass below 80 should result in smoother and more balanced response in the system. You may prefer more "boom" overall so feel free to adjust the subwoofer channel level or better yet the bass/treble tone controls to tweak to taste.
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What is the purpose of running Audyssey if I'm going to go by most recommendations and change the "Full Band" settings to 80Hz THX (small) or to what sounds best to me?
The purpose of Audyssey is to equalize/filter your speakers to account for the acoustics of your room, so your system is providing a flat response overall and you can hear movie soundtracks as the director/mixer intended.
Once you have run Audyssey, you can then tweak things like crossovers, speaker volumes, etc. and Audyssey's EQ filters will still be operating to account for the acoustics of your room.
You should ALWAYS set the LFE LPF to 120Hz. On your setup, an 80Hz xover all around for the speakers will probably work great, although you could put the mains at 60 if you want and see how you like it.
Another recommendation, since Audyssey set your subs to -9db, is that the gain dials on your subs may be too high as Audyssey is really trying to trim it down. Try turning down the volumes on the two subs a bit, and then re-run Audyssey. Make sure to keep the room quiet and use a tripod for the mic, and actually get that mic at ear level and away from flat surfaces (like walls and couch cushions).
Then, after running Audyssey, set LFE LPF to 120 and the other crossovers to 80. Play some music with good bass and play with the bass/treble controls and tweak to taste. Then throw on a movie with some good bass scenes and see how it sounds.